Source Code for Module Chem.SATIS

  1  # $Id: SATIS.py 2 2006-05-06 22:54:39Z glandrum $ 
  2  # 
  3  # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """  Functionality for SATIS typing atoms 
  8   
  9  """ 
 10  import Chem 
 11   
 12  _debug = 0 
 13   
 14  # 
 15  #  These are SMARTS patterns for the special cases used in 
 16  #  SATIS typing. 
 17  # 
 18  aldehydePatt = Chem.MolFromSmarts('[CD2]=[OD1]') 
 19  ketonePatt = Chem.MolFromSmarts('[CD3]=[OD1]') 
 20  amidePatt = Chem.MolFromSmarts('[CD3](=[OD1])-[#7]') 
 21  esterPatt = Chem.MolFromSmarts('C(=[OD1])-O-[#6]') 
 22  carboxylatePatt = Chem.MolFromSmarts('C(=[OD1])-[OX1]') 
 23  carboxylPatt = Chem.MolFromSmarts('C(=[OD1])-[OX2]') 
 24   
 25  specialCases = ((carboxylatePatt,97), 
 26                  (esterPatt,96), 
 27                  (carboxylPatt,98), 
 28                  (amidePatt,95), 
 29                  (ketonePatt,94), 
 30                  (aldehydePatt,93)) 
 31   
 32   
 33 -def SATISTypes(mol,neighborsToInclude=4): 
 34    """ returns SATIS codes for all atoms in a molecule 
 35   
 36     The SATIS definition used is from: 
 37     J. Chem. Inf. Comput. Sci. _39_ 751-757 (1999) 
 38   
 39     each SATIS code is a string consisting of _neighborsToInclude_ + 1 
 40     2 digit numbers 
 41   
 42     **Arguments** 
 43   
 44       - mol: a molecule 
 45   
 46       - neighborsToInclude (optional): the number of neighbors to include 
 47         in the SATIS codes 
 48   
 49     **Returns** 
 50   
 51       a list of strings nAtoms long 
 52   
 53    """ 
 54    global specialCases 
 55     
 56    nAtoms = mol.GetNumAtoms() 
 57    atomicNums = [0]*nAtoms 
 58    atoms = mol.GetAtoms() 
 59    for i in xrange(nAtoms): 
 60      atomicNums[i] = atoms[i].GetAtomicNum() 
 61   
 62    nSpecialCases = len(specialCases) 
 63    specialCaseMatches = [None]*nSpecialCases 
 64    for i,(patt,idx) in enumerate(specialCases): 
 65      if mol.HasSubstructMatch(patt): 
 66        specialCaseMatches[i] = mol.GetSubstructMatches(patt) 
 67      else: 
 68        specialCaseMatches[i] = () 
 69       
 70    codes = [None]*nAtoms 
 71    for i in range(nAtoms): 
 72      code = [99]*(neighborsToInclude+1) 
 73      atom = atoms[i] 
 74      atomIdx = atom.GetIdx() 
 75      code[0] = min(atom.GetAtomicNum(),99) 
 76      bonds = atom.GetBonds() 
 77      nBonds = len(bonds) 
 78      otherIndices = [-1]*nBonds 
 79      if _debug: print code[0], 
 80      for j in range(nBonds): 
 81        otherIndices[j] = bonds[j].GetOtherAtom(atom).GetIdx() 
 82        if _debug: print otherIndices[j], 
 83      if _debug: print   
 84      otherNums = [atomicNums[x] for x in otherIndices] + \ 
 85                  [1]*atom.GetTotalNumHs() 
 86      otherNums.sort() 
 87   
 88      nOthers = len(otherNums) 
 89      if nOthers > neighborsToInclude: 
 90        otherNums.reverse() 
 91        otherNums = otherNums[:neighborsToInclude] 
 92        otherNums.reverse() 
 93        for j in range(neighborsToInclude): 
 94          code[j+1] = min(otherNums[j],99) 
 95      else: 
 96        for j in range(nOthers): 
 97          code[j+1] = min(otherNums[j],99) 
 98        if nOthers < neighborsToInclude and code[0] in [6,8]: 
 99          found = 0 
100          for j in range(nSpecialCases): 
101            for matchTuple in specialCaseMatches[j]: 
102              if atomIdx in matchTuple: 
103                code[-1] = specialCases[j][1] 
104                found = 1 
105                break 
106            if found: 
107              break 
108           
109      codes[i] = ''.join(['%02d'%(x) for x in code]) 
110    return codes 
111   
112  if __name__ == '__main__': 
113    smis = ['CC(=O)NC','CP(F)(Cl)(Br)(O)', 
114            'O=CC(=O)C','C(=O)OCC(=O)O','C(=O)[O-]'] 
115    for smi in smis: 
116      print smi 
117      m = Chem.MolFromSmiles(smi) 
118      codes = SATISTypes(m) 
119      print codes 
120